Phineas and Ferb: Civil War
by Jabuscus
Summary: After a contraption Phineas and Ferb built fell, The two are at odds trying to decide what to do about it. Ferb want's to sign his inventing rights to the government, helping them build things they never could for the good of the country. Phineas on the other hand, believes you should be able to build freely, and spread your wings. Now everyone must Choose A Side.
1. The Accident

**Note: All character are now 18 years or older depending on the character, there are also marvel characters involved, you could say it's a sequel to mission marvel**.

hapter 1: The Accident.

"Ferb pass me the blow torch." Phineas Flynn told his stepbrother.

Alot had happened since thier second vist to the second dimension, where they found Phineas' clone, Jalen, and went back home. Phineas was now a more serious in serious situations, learning from his clone how to take action when something needs to be done. Since Jalen worked at S.H.E.I.L.D, (by request of Nick Fury, due to his skill set.) Phineas got access to the helicarrier once, meeting one of his heroes, Captain America, he took a liking to Cap, asking him advice on leadership and what's wrong and right. Fury even got him an exact shield replica for Christmas, for his work on saving earth once or twice and all.

Ferb, doing the complete opposite, took a liking to Iron Man, taking the internship offer he got all those years ago. He helped Tony build suits and gadgets, even helping out bulding Stark tower. He also made his own personal Iron Man suit, with help from Tony of course.

Isabella hadn't changed all that much, now being in a relationship with Phineas, after all her anticipation built up of years, didn't need anything else. Now being too old to be a fireside girl, still has her troop of friends with her, often going to thier old lodge to help out the next generation of fireside girls.

Nothing really changed with Buford and Baljeet, still have their frenemy relationship going on.

Candace had changed too, not being so obsessive about busted her brothers, now going to college at Danville University, still dating Jeremy.

Ferb handed him the blow torch, and continued on his side of the project

"Hey Phineas, What'cha'doin." Isabella, Phineas' girlfriend asked.

"Hey Isabella, just building the coolest thing ever, it's a building where, when you go into a room, you could end up anywhere. For example, you could be in a park, then go into another room and be in Canada." He responded.

"Cool." She responded.

-S.H.E.I.L.D. Helicarrier-

"Mission complete Fury." Jalen said putting some files down on Fury's desk.

After the second dimension incident, he decided to return home with Phineas. That's when Nick Fury offered him a job at S.H.E.I.L.D., knowing his past.

"Excellent work Flynn." He responded saluting to him.

-Phineas and Ferb's backyard.-

"It's done, let's go check it out." Buford said running inside, and everyone followed.

Little did they know, a few of the blots in the building weren't screwed on right.

"This is amazing." Baljeet said. That's when the building began to shake.

Phineas looked outside to see that one of the support pillars fell, taking the building down with it.

"Everyone get down!" He yelled, and everyone fell to the ground... then the building did.

"...eas...phineas...PHINEAS!" Isabella yelled, as Phineas woke up from his trance.

He slowly got up, noticing the rubble around him.

"Is everyone ok?" He asked her.

"Yeah, but Buford broke his arm, and Baljeet's face got cut real bad, we called an ambulance, their at the hospital." Ferb responded for her.

Phineas was standing in front of the carnage looking stern, with a disappointed Ferb standing behind him.

-The Pentagon-

"Sir, a giant building in Danville made by those two boys has just collapsed." A special agent said.

"This is the oppurtunity we've been waiting for, let's get over there now." A general said.

That's chapter one of Civil War.

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See you soon.


	2. The Contract Part 1

**Note: All character are now 18 years or older depending on the character, there are also marvel characters involved, you could say it'sa sequel to mission marvel**

Chapter 2: The Contract.

Phineas was still standing there, looking on at the chaos, he couldn't belive what happened.

"This is all my fault, I should have done an inspection to make sure everything was ok, I-" Phineas befan blamed himslef before Isabella cut him off.

"Don't do that, all of us built it, we're all responsible for what hppened, I just hope we didn't affect alot of people." She said lighthearted.

That's when Phineas heard sirens coming, getting lounder and louder by the second, until they finally reached his driveway.

"Put your hands in the air!" A cop screamed.

Phineas looked at Isabella, then to Ferb, then slowly got on his knees, putting his hands in the air. Isabella and Ferb followed. Three came handcuffing all of them, putting them in a cop car, then driving away.

-S.H.E.I.L.D. Helicarrier.-

"So... How's life.?" Jalen asked Hulk.

"Pretty angry, pretty angry." He responded.

"I don't think-" He was cut off by a news Alert.

"Hello, I'm Rick Sanchez, I'm here at a new station reading a monitor, it says a contraption built by Phineas Flynn, Ferb Fletcher, and others has collapsed. I could do way better, but anyways, the two boys and a friend are now in custody." The news anchor said.

"I gotta go." He told Hulk, running game away. The Hulk simply shrugged.

-Danville Police Station-

"You kids are in trouble." The policeman told them.

"Look we're sorry, we can-" Phineas started.

"Sorry? You think a sorry is gonna cut it, do you know how many casualties there could have been, the collateral damage?" The cop got on to him, then another one entered, whispering into his ear. They both then walked out of the room. And another man entered.

"Hello kids, my name is General Ross, I'm here to make a proposition for you." The man said.

"... What kind of proposition?" Isabella asked.

"You see, I've been watching you, listening to you, seeing everything you've bulit, amazing by the way. Despite my worry, I can't stop you from buliding, never had a reason to, until this happened." Ross then turned on the tv in the room, showing the recent devisation.

The three looked in horror as they saw houses destroyed, some on fire. Then it cut to a live feed of a child, crying, because on the floor next to her was her mother, dead on the floor. It was even more horrible when they saw officials struggling the get the girl away from the body. Isabella turned away from the tv crying, Phineas then started comforting her.

"Shut it off." Ferb said, knowing how upset his friend was

"Because of this recent tragedy, we've decidied to give you a chance to right this wrong."

General Ross then pulled out a file.

"It's the Inventing Registration Act. By signing this, you agree you build for the government and help your country, and so we can keep a close eye on you. Sign it, and this will all blow over." Ross said.

"But we need a signature from everyone who has ever been involved with the creation of one of you're inventions. We'll give you time to think about it. However if you do not, there will be consequences

Then two policemen entered.

"You have three hours to think it over, we'll escort you home. With police survelancing until the time limit is up of course."

Those were the final words spoken by the general before he left the room.

The trio of friends looked at each other, wondering what the others were voting to do.

 **Hope you enjoyed, leave a review and tell me what you thought, follow and favorite if you like the story.**

 **Jabuscus is out, peace.**


	3. The Contract Part 2

Chapter 3: The Contract Part 2

 **Note: All character are now 18 years or older depending on the character, there are also marvel characters involved, you could say it'sa sequel to mission marvel.**

After they rounded everyone up, they discussed.

"Signing this thing is the right thing to do. Think about what could happen next time." Doctor Doofenshmirtz said.

"What could happen next? Think about what they'll make us do, build weapons or nombs, or sports equipment!" Baljeet replied.

"Building sports equipment is better than sitting in a cell for the rest of our lives, also, why sports equipment?" Vanessa asked.

"I do not know what government agents do during their free time." He defended.

"Guys think about this, what happens when we wanna build something but they don't let us, what if they want us to build them something but we don't think it's a good idea." Phineas stated to everyone.

"It doesn't matter, if they want us to do something, then we do it." Ferb told Phineas, sitting back in the chair he was in.

"But-" Phineas was about to respond.

"Phineas, as much as I hate going against you... Ferb is right." Isabella said.

Phineas stood there in silence, in shock, everyone was, even Ferb.

"C'mon Phineas, don't do this. Think of what would happen to you." Isabella said said looking him right in the eyes.

Phineas, feeling mixed emotions on what she thought, was about to respond, but before he could even think of what to say, there was then a knock at the door. Phineas opened it to see General Ross standing there.

"Alright boys I'm just gonna cut to the chase, did you make a decision?" He asked.

Ferb stepped forward.

"Yes we did sir." He replied.

"Exellent." Ross put the contract on the table, and gave Ferb a pen. He didn't hesitate to sign it. Soon after, Vanessa, Buford, Dr.D and even Isabella signed.

"Phineas, are you ready sign?" The general asked.

"Of course he is, here Phineas." Isabella said, handing him a pen, and the contract.

Phineas just stared blankly at the items in his hands, while everyone watched in curiosity, fear, and fear.

"Phineas, is there a problem?" Ross asked.

"... Yeah, as a matter of fact, there is a problem." He replied.

"Well, what is it?"

"This contract."

Phineas then threw to contract back at the table.

"Phineas, don't be a fool, sign it." Ferb told him.

Phineas just stood there for a few moments, then turned his backing, going to walk away. Ferb grabbed his shoulder and turned him around, they were literally face to face.

"SIGN THE CONTRACT PHINEAS!" HE yelled at him.

Then the thing that no one thought would happen happened. Phineas pushed Ferb off him.

"... No Ferb." He said, with tears in his eyes. Ferb looked at him shocked.

"Phineas is right, I'm not going to give away my freedom." Baljeet said, standing next to him.

"I always liked Phineas better than Ferb anyway." Irving said, standing next to Baljeet.

"Yeah, I'm with Phineas too." Candace said, standing next to the opposite end of Phineas.

"... Well you made your choice... Arrest them." Ross said into a walkie talkie.

"SHIT, RUN!" Phineas yelled, running out if the house with all the others who chose not to sign.

"Candace, lead them to the woods, Baljeet knows a safe place there, me and him built it in case something bad ever happened, we're the only ones who know where it is." Phineas told his older sister.

"What are you gonna do?" She asked.

"I'll distract them and lead them the other way, NOW GO!" He yelled as they split up into different directions.

"Alright, come and get me." Phineas thought to himself.

 **Well after a long absence I've returned with another chapter.**

 **I hoped you enjoyed.**

 **Leave areview, favorite the story, and follow the account.**


	4. The Chase

Chapter 4: The Chase

 **Note: All character are now 18 years or older depending on the character, there are also marvel characters involved, you could say it'sa sequel to mission marvel.**

Phineas ran down the streets, not even caring where he was going, he just ran, and ran, and ran. He stopped to catch his breath, then a police car pulled up, the officer stepped out of his car, gun in hand.

Phineas' eyes widened, he didn't have a plan, he was just improvising, he just stood there in fear.

"Phineas Flynn, put your hands in the air and get on the ground!" He said.

Phineas didn't know what to do, so he slowly complied. The officer stepped towards him, getting out hand cuffs. Phineas then pulled something on the watch that he was wearing.

"AHH BRAIN FREEZE!" The officer yelled. Phineas pushed him down, got in the officers car, and sped off.

"Ok.. ok.. I stole a cop car, I'm wanted, and I'm at odds with my brother... I've been through worse.

He was driving for a few moments, then someone spoke in the radio in the car.

"Phineas, pull over and turn yourself in, this dosent have to end bad." Isabella's voice spoke through the radio. Tears filled Phineas' eyes as he turned off the radio. He couldn't belive what Isabella did, siding with Ferb over him. After everything they've been through, all the lsughs, the tears the words... and she chose the other side. He silently cried.

Then he heard sirens, turning his head back, he saw police cars behind him.

"Crap, there must be a GPS in the car." He thought, wiping away the tears.

He looked forward noticing that there were train tracks... and an upcoming train.

"Alright Phineas, lets do something cliché." He told himself. He accelerated the car, the train coming close. He closed his eyes, not wanting to see what would happen. The car touched the tracks... And he made it, leaving the other cops on the other side of the tracks.

"YES, I DID IT, FOR A SECOND I THOUGHT THAT-" He was yelling, then another police car rammed into the side of his. The car flipped a few times before stopping.

For a few moments there was darkness, and all he heard was a high pitched noise, then the noise went down, and he could see again, he was badly wounded, and still straped to his seatbelt. The car was upside down, so he slowly unbuckled his seatbelt, falling hard onto the top of the inside of the car.

Phineas slowly opened the door, litterally falling out of the car. He slowly stood up, seeing five cars, and eight cops around him.

Knowing he was beat, he got on the ground. A cop approched him.

"You got heart kid, but made the wrong choice." He said, and just as he grabbed Phineas, he fell to the ground. Phineas looked at him, seeing a hole in his head.

He was shot.

Phineas staggered back out of fear not knowing what was going on.

Then... one by one... All the other cops were shot and fell to the ground. Phineas saw the outline of a person approach him. One of the cops started crawling away, the figure pulled out a pistol, shooting the cop twice. The figure then looked at Phineas, and that's when he got a good look at it.

"Jesus... Jalen." He said, then passing out.

 **Wow, what a cliffhanger, am I right.**

 **Hope you enjoyed the chapter.**

 **Leave a review. Follow the account, favorite the story.**

 **Jabuscus is out, peace**


	5. Team Phineas

**Note: All character are now 18 years or older depending on the character, there are also marvel characters involved, you could say it'sa sequel to mission marvel.**

Chapter 5: Team Phineas

Phineas stirred awake, finding out that he was in the passengers seat of a car, he looked to his left to see his cyborg clone Jalen sitting in the driving seat.

Phineas didn't know what was going on, so he finally spoke up.

"What happened.?"

Jalen turned his head slightly at him, then looking back at the road.

"You were totally screwed, I saved you." He responded.

"What?!"

"Yeah, you were driving from the cops, they ran into you and they were going to arrest you, I had to do something, I couldn't just let you go to jail."

Phineas looked around at his surroundings, all he saw was trees.

"Where are we?" Phineas asked.

"We're going to your secret hideout in the woods."

Phineas snapped up.

"How do you know about that?" The only people that could possibly know about it were him and Baljeet, they bulit it as a plan b in case something ever happened, and they swore never to tell anyone.

"I work for S.H.I.E.L.D. now, I know alot of things." He responded, stopping the car.

"We're here." He said, getting out of the car. Phineas got out as well seeing what most people saw as an old wore out shed, but the interior was beautiful.

Jalen opened the door, and walked in.

"Hey it's me and Phineas, come out." Jalen said walking in, with Phineas behind him.

"Oh thank god." They heard, seeing Candace, Baljeet, and Irving come out of the shadows.

"Is this really it?" Jalen asked.

"Yeah." Phineas responded, walking past him.

"Well, looks like Ferb has the numbers game, meaning he has the advantage. We're going to have to devise a plan of attack on Ferb's side, first we'll need-" Jalen was starting to get into detail but Phineas cut him off.

"Attack?... attack? What you mean, you think we're gonna to fight, we're not gonna do that, we're all basically family, I'm sorry but we're going to have to wait for all of this to blow over." Phineas said seriously.

Jalen stood there silently. Everyone was waiting for a response. Then he started laughing histarically.

"Ha..ha... blow over. You really think this is gonna blow over, this is staying... Forever. We have to act now."

Everyone was confused.

"Why do we need to act now?" Baljeet asked.

"I work for S.H.I.E.L.D, we have eyes and ears everywhere, I have intel that the program that General Ross runs is using everyone for their skills to build a weapon of mass destruction that could kill anyone and everyone, they were just waiting for a reason for you to be so desperate to agree to their terms." Jalen explained.

"So your saying that everyone who signed is making a weapon?" Irving tried to recap on everything

"Yes."

"...So what do we do?" Candace asked.

"... You plan."

"Wait we? Aren't you staying?" Phineas asked with confusion.

"I'm not one to choose sides, I'm giving you my honest opinion on what to do." Jalen said starting to walk away.

"Oh one more thing, if stuff gets too out of hand, S.H.E.I.L.D told me I'm going to be the one to take the case, so don't mess up."

That was the final thing he said before leaving.

"Alright, let's get to work, Irving set up blueprints on the computer, Baljeet your with me, Candace you're on news coverage, if anything involving Ross happens I wanna be the first to know about it." He said, already making a plan in his head.

Then the door slightly opened, and Jalen slowly came back in.

"That reminds me, you want another member for your team?" Jalen asked.

"Yes that could be useful!" Phineas almost yelled.

"Alright, just let me get him." Then he left again.

-Somewhere in San Francisco-

Scott Lang was laying in bed in his apartment when there was a knock at the door. He slowly got up and the knocking continued.

"Alright alright I'm coming." He said blindly opening the door. Then he saw a blur because he had just got up

"Hey what's up, I ordered my pizza like 40 minutes ago and, wait a minute your not a pizza guy." He said as the blur slowly formed into a familiar colleague.

"Oh hey, what's up, another mission?" He asked.

" Sort of, look, my clone needs help, but I can't help him, I'm with S.H.I.E.L.D and I can't interfere unless I'm told, can you help a brother out?" Jalen asked.

"Sure, as soon as my pizza gets here." He said.

Jalen then picked up a pizza from the ground.

"Get the suit let's go." Jalen said walking away.

Scott just slowly looked at the pizza.

"How did he get this?"

 **Done with this chapter, this story is way over due, I'll try to write more.**

 **Leave a review, favorite the story, follow the account.**

 **Peace.**


	6. Team Ferb

**Note: All character are now 18 years or older depending on the character, there are also marvel characters involved, you could say it'sa sequel to mission marvel.**

Chapter 6: Team Ferb

Ferb was sitting at the table in the house, Phineas and everyone just ran away, and Ferb didn't know what to think. Does he feel anger at Phineas for declining to sign the accords, or sad that half of his friends are now wanted.

Vanessa approached Ferb slowly, not knowing what to say.

"Hey, I'm sure they'll catch him, then Ross will ask him a second time. Then he'll have to say yes." She assured him.

"Ha... no, I know Phineas, when he makes up his mind once, it stays." He replied.

"How's Isabella?" Ferb asked.

"Still crying like a baby." Buford responded.

Ferb gave him a glare, and Buford kept quiet.

"I'll go talk to her." Ferb assured everyone.

He got out of his seat and proceeded up to Phineas' room, where Isabella was, crying on Phineas' bed. She saw him walk in, but continuted to cry. Ferb oulled out his handkerchief, the same one he had given her so many times, and handed it to her. She took it quickly.

"Thanks Ferb, I just don't know what to do, I mean, I thought that he would look into reason. How are me and him going to make a life together if he's in prison, why did he choose the wrong side?!" She yelled, crying heavily.

"And now he doesn't trust me anymore, where does this leave our relationship, he's going to dump me, after all my waiting, I finally get him, and now he's going to dump, me, why, why did you have to do this Phineas!" She shrieked crying some more.

Ferb didn't know what to say, so he grabbed Isabella's head, turning it towardshim, staring in her eyes, as if saying, _Look, everythings going to be ok._ It made her feel better, at least enough to make her stop crying.

Ferb got up and offered her his _y_ hand, which she took. They both headed downstairs where everyone else was. Ross entered tge house shortly after.

"They got away, apparently some guy shot everyone down, and took Phineas after they had him surrounded." He stated, then giving Ferb a tablet, showing him the footage.

"Hey, that's that wannabe clone Phineas, Jalen." Buford said, seeing the footage.

"Yeah, he works for S.H.I.E.L.D, trained assasin cyborg." Ferb said, giving Ross the tablet back.

"Well my men will find them, all of them, until then, everyone pack your bags, I'll show you where your going to be staying for a couple of days, there's something we need you to build." Ross said to everyone.

They were quiet confused, not expecting them wanting to do something so quickly, but Ferb gave him a salute as if saying, _Yes sir!._

Ross walked away, then coming back to say something else.

"By the way, I've hired you some protection just in case that Jalen character comes back."

"Who?" Dr.D asked.

Then, a dark figure appered from out of nowhere, standing in front of everyone. He was wearing all black, with silver on it, tgat looked like metal. His hands and feet had claws, his head also looked like some sort of cat.

"So you like cats?" Buford asked.

"If I had a nickel for every time I heard that." The man said said.

"Meet the Black Panther, he'll be your protection until all of this ends." Ross said walking away, as the Black Panther followed.

The group looked at the new team member, rememvering him.

" Ten minutes... Get what you need." Ferb said, walking into his house, getting ready to pack his bags.


End file.
